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Volumn 7, Issue 1, 2014, Pages

Microbial diversity in fecal samples depends on DNA extraction method: EasyMag DNA extraction compared to QIAamp DNA stool mini kit extraction

Author keywords

Denaturing gradient gel electrophoresis; DNA measurement; easyMag ; Fecal DNA extraction; Inflammatory bowel disease; NanoDrop ; QIAamp DNA stool mini kit; Qubit system

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; MICROSPHERE; RNA 16S; SILICON DIOXIDE;

EID: 84892586947     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-7-50     Document Type: Article
Times cited : (59)

References (26)
  • 1
    • 0037425743 scopus 로고    scopus 로고
    • Gut flora in health and disease
    • DOI 10.1016/S0140-6736(03)12489-0
    • Gut flora in health and disease. Guarner F, Malagelada JR, Lancet 2003 361 512 519 10.1016/S0140-6736(03)12489-0 12583961 (Pubitemid 36173720)
    • (2003) Lancet , vol.361 , Issue.9356 , pp. 512-519
    • Guarner, F.1    Malagelada, J.-R.2
  • 2
    • 79960067123 scopus 로고    scopus 로고
    • Human gut microbiota and its relationship to health and disease
    • 10.1111/j.1753-4887.2011.00402.x 21729093
    • Human gut microbiota and its relationship to health and disease. Wallace TC, Guarner F, Madsen K, Cabana MD, Gibson G, Hentges E, Sanders ME, Nutr Rev 2011 69 392 403 10.1111/j.1753-4887.2011.00402.x 21729093
    • (2011) Nutr Rev , vol.69 , pp. 392-403
    • Wallace, T.C.1    Guarner, F.2    Madsen, K.3    Cabana, M.D.4    Gibson, G.5    Hentges, E.6    Sanders, M.E.7
  • 4
    • 0036135946 scopus 로고    scopus 로고
    • Molecular monitoring of succession of bacterial communities in human neonates
    • DOI 10.1128/AEM.68.1.219-226.2002
    • Molecular monitoring of succession of bacterial communities in human neonates. Favier CF, Vaughan EE, De Vos WM, Akkermans AD, Appl Environ Microbiol 2002 68 219 226 10.1128/AEM.68.1.219-226.2002 11772630 (Pubitemid 34031183)
    • (2002) Applied and Environmental Microbiology , vol.68 , Issue.1 , pp. 219-226
    • Favier, C.F.1    Vaughan, E.E.2    De Vos, W.M.3    Akkermans, A.D.L.4
  • 5
    • 0000374167 scopus 로고    scopus 로고
    • Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples
    • Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples. Abu Al-Soud W, Radstrom P, Appl Environ Microbiol 1998 64 3748 3753 9758794 (Pubitemid 28462967)
    • (1998) Applied and Environmental Microbiology , vol.64 , Issue.10 , pp. 3748-3753
    • Abu Al-Soud, W.1    Radstrom, P.2
  • 6
    • 0030048084 scopus 로고    scopus 로고
    • Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein
    • Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Kreader CA, Appl Environ Microbiol 1996 62 1102 1106 8975603 (Pubitemid 26071491)
    • (1996) Applied and Environmental Microbiology , vol.62 , Issue.3 , pp. 1102-1106
    • Kreader, C.A.1
  • 8
    • 0033989325 scopus 로고    scopus 로고
    • Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers
    • Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers. Walter J, Tannock GW, Tilsala-Timisjarvi A, Rodtong S, Loach DM, Munro K, Alatossava T, Appl Environ Microbiol 2000 66 297 303 10.1128/AEM.66.1.297-303. 2000 10618239 (Pubitemid 30030531)
    • (2000) Applied and Environmental Microbiology , vol.66 , Issue.1 , pp. 297-303
    • Walter, J.1    Tannock, G.W.2    Tilsala-Timisjarvi, A.3    Rodtong, S.4    Loach, D.M.5    Munro, K.6    Alatossava, T.7
  • 9
    • 0030748867 scopus 로고    scopus 로고
    • Inhibition and facilitation of nucleic acid amplification
    • Inhibition and facilitation of nucleic acid amplification. Wilson IG, Appl Environ Microbiol 1997 63 3741 3751 9327537 (Pubitemid 27411322)
    • (1997) Applied and Environmental Microbiology , vol.63 , Issue.10 , pp. 3741-3751
    • Wilson, I.G.1
  • 10
    • 0033778621 scopus 로고    scopus 로고
    • Evaluation of a PCR primer based on the isocitrate dehydrogenase gene for detection of Helicobacter pylori in feces
    • 11015397
    • Evaluation of a PCR primer based on the isocitrate dehydrogenase gene for detection of Helicobacter pylori in feces. Argyros FC, Ghosh M, Huang L, Masubuchi N, Cave DR, Grubel P, J Clin Microbiol 2000 38 3755 3758 11015397
    • (2000) J Clin Microbiol , vol.38 , pp. 3755-3758
    • Argyros, F.C.1    Ghosh, M.2    Huang, L.3    Masubuchi, N.4    Cave, D.R.5    Grubel, P.6
  • 11
    • 33846057772 scopus 로고    scopus 로고
    • Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples
    • DOI 10.1016/j.mcp.2006.08.003, PII S0890850806000594
    • Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples. Whitehouse CA, Hottel HE, Mol Cell Probes 2007 21 92 96 10.1016/j.mcp.2006.08.003 17011748 (Pubitemid 46074388)
    • (2007) Molecular and Cellular Probes , vol.21 , Issue.2 , pp. 92-96
    • Whitehouse, C.A.1    Hottel, H.E.2
  • 12
    • 2442510059 scopus 로고    scopus 로고
    • Improved extraction of PCR-quality community DNA from digesta and fecal samples
    • Improved extraction of PCR-quality community DNA from digesta and fecal samples. Yu Z, Morrison M, Biotechniques 2004 36 808 812 15152600 (Pubitemid 38620199)
    • (2004) BioTechniques , vol.36 , Issue.5 , pp. 808-812
    • Yu, Z.1    Morrison, M.2
  • 13
    • 79951879778 scopus 로고    scopus 로고
    • Five commercial DNA extraction systems tested and compared on a stool sample collection
    • 10.1016/j.diagmicrobio.2010.09.023 21353945
    • Five commercial DNA extraction systems tested and compared on a stool sample collection. Persson S, De Boer RF, Kooistra-Smid AM, Olsen KE, Diagn Microbiol Infect Dis 2011 69 240 244 10.1016/j.diagmicrobio.2010.09.023 21353945
    • (2011) Diagn Microbiol Infect Dis , vol.69 , pp. 240-244
    • Persson, S.1    De Boer, R.F.2    Kooistra-Smid, A.M.3    Olsen, K.E.4
  • 14
    • 84873717548 scopus 로고    scopus 로고
    • The biodiversity and composition of the dominant fecal microbiota in patients with inflammatory bowel disease
    • 23276768
    • The biodiversity and composition of the dominant fecal microbiota in patients with inflammatory bowel disease. Sha S, Xu B, Wang X, Zhang Y, Wang H, Kong X, Zhu H, Wu K, Diagn Microbiol Infect Dis 2012 75 245 251 23276768
    • (2012) Diagn Microbiol Infect Dis , vol.75 , pp. 245-251
    • Sha, S.1    Xu, B.2    Wang, X.3    Zhang, Y.4    Wang, H.5    Kong, X.6    Zhu, H.7    Wu, K.8
  • 15
    • 36348983382 scopus 로고    scopus 로고
    • Comparative evaluation of in-house manual, and commercial semi-automated and automated DNA extraction platforms in the sample preparation of human stool specimens for a Salmonella enterica 5'-nuclease assay
    • DOI 10.1016/j.mimet.2007.09.003, PII S0167701207002941
    • Comparative evaluation of in-house manual, and commercial semi-automated and automated DNA extraction platforms in the sample preparation of human stool specimens for a Salmonella enterica 5′-nuclease assay. Schuurman T, De BR, Patty R, Kooistra-Smid M, Van ZA, J Microbiol Methods 2007 71 238 245 10.1016/j.mimet.2007.09.003 17942177 (Pubitemid 350151516)
    • (2007) Journal of Microbiological Methods , vol.71 , Issue.3 , pp. 238-245
    • Schuurman, T.1    De Boer, R.2    Patty, R.3    Kooistra-Smid, M.4    Van Zwet, A.5
  • 16
    • 33646128006 scopus 로고    scopus 로고
    • Efficient methods for sample processing and cDNA synthesis by RT-PCR for the detection of grapevine viruses and viroids
    • 10.1016/j.jviromet.2006.01.016 16510197
    • Efficient methods for sample processing and cDNA synthesis by RT-PCR for the detection of grapevine viruses and viroids. Nakaune R, Nakano M, J Virol Methods 2006 134 244 249 10.1016/j.jviromet.2006.01.016 16510197
    • (2006) J Virol Methods , vol.134 , pp. 244-249
    • Nakaune, R.1    Nakano, M.2
  • 17
    • 79955812835 scopus 로고    scopus 로고
    • Optimising bacterial DNA extraction from faecal samples: Comparison of three methods
    • doi: 10.2174/1874285801105010014. Epub;%2011 Apr 22. 14 - 17 10.2174/1874285801105010014 21643498
    • Optimising bacterial DNA extraction from faecal samples: comparison of three methods. Smith B, Li N, Andersen AS, Slotved HC, Krogfelt KA, Open Microbiol J 2011 5 14 7 doi: 10.2174/1874285801105010014. Epub;%2011 Apr 22.: 14-17 10.2174/1874285801105010014 21643498
    • (2011) Open Microbiol J , vol.5 , pp. 14-17
    • Smith, B.1    Li, N.2    Andersen, A.S.3    Slotved, H.C.4    Krogfelt, K.A.5
  • 18
    • 84875855272 scopus 로고    scopus 로고
    • Is supplementary bead beating for DNA extraction from nematode eggs using the NucliSENS(R) easyMag(R) protocol necessary?
    • 10.1128/JCM.03353-12 23325821
    • Is supplementary bead beating for DNA extraction from nematode eggs using the NucliSENS(R) easyMag(R) protocol necessary? Andersen LO, Roser D, Nejsum P, Nielsen HV, Stensvold CR, J Clin Microbiol 2013 51 1345 1347 10.1128/JCM.03353-12 23325821
    • (2013) J Clin Microbiol , vol.51 , pp. 1345-1347
    • Andersen, L.O.1    Roser, D.2    Nejsum, P.3    Nielsen, H.V.4    Stensvold, C.R.5
  • 21
    • 84894900812 scopus 로고    scopus 로고
    • ConferenceSeries 307 edition
    • 1Drop Technology Ltd. Tallaght Business Park, Whitestown, Dublin 24, Ireland: IOP Publishing McPartlin KASRNM J
    • ConferenceSeries 307 edition. O'Neill M, Comparison of the TLDA with the Nanodrop and the reference Qubit system 1Drop Technology Ltd., Tallaght Business Park, Whitestown, Dublin 24, Ireland: IOP Publishing, McPartlin KASRNM J, 2012 1 6
    • (2012) Comparison of the TLDA with the Nanodrop and the Reference Qubit System , pp. 1-6
    • O'Neill, M.1
  • 22
    • 67650901965 scopus 로고    scopus 로고
    • Is habitual alcohol drinking associated with reduced electrophoretic DNA migration in peripheral blood leukocytes from ALDH2-deficient male Japanese?
    • 10.1093/mutage/gep008 19286920
    • Is habitual alcohol drinking associated with reduced electrophoretic DNA migration in peripheral blood leukocytes from ALDH2-deficient male Japanese? Lu Y, Morimoto K, Mutagenesis 2009 24 303 308 10.1093/mutage/gep008 19286920
    • (2009) Mutagenesis , vol.24 , pp. 303-308
    • Lu, Y.1    Morimoto, K.2
  • 23
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Muyzer G, De Waal EC, Uitterlinden AG, Appl Environ Microbiol 1993 59 695 700 7683183 (Pubitemid 23072343)
    • (1993) Applied and Environmental Microbiology , vol.59 , Issue.3 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 24
    • 79955935457 scopus 로고    scopus 로고
    • Intestinal microbiota in inflammatory bowel disease: Friend of foe?
    • 10.3748/wjg.v17.i5.557 21350704
    • Intestinal microbiota in inflammatory bowel disease: friend of foe? Fava F, Danese S, World J Gastroenterol 2011 17 557 566 10.3748/wjg.v17.i5.557 21350704
    • (2011) World J Gastroenterol , vol.17 , pp. 557-566
    • Fava, F.1    Danese, S.2
  • 25
    • 77957603468 scopus 로고    scopus 로고
    • The role of bacteria in the pathogenesis of inflammatory bowel disease
    • 10.5009/gnl.2010.4.3.295 20981205
    • The role of bacteria in the pathogenesis of inflammatory bowel disease. Friswell M, Campbell B, Rhodes J, Gut Liver 2010 4 295 306 10.5009/gnl.2010.4.3. 295 20981205
    • (2010) Gut Liver , vol.4 , pp. 295-306
    • Friswell, M.1    Campbell, B.2    Rhodes, J.3


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